data_2R86 # _model_server_result.job_id ocueQrQXewfR-3T7EKfD0w _model_server_result.datetime_utc '2024-11-27 13:00:08' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 2r86 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":501}' # _entry.id 2R86 # _exptl.entry_id 2R86 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.174 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4S)-2-METHYL-2,4-PENTANEDIOL _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 2R86 _cell.length_a 122.477 _cell.length_b 122.477 _cell.length_c 560.925 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2R86 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,M 1 1,2,3 B,I,J,K,L,N 2 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 122.477 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 61.2385 106.068193 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 G N N ? 5 H N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A O GLU 98 A GLU 98 1_555 E NA NA . A NA 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? metalc ? metalc2 A O ILE 284 A ILE 284 1_555 E NA NA . A NA 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc3 E NA NA . A NA 600 1_555 M O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.721 ? metalc ? metalc4 E NA NA . A NA 600 1_555 M O HOH . A HOH 673 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? metalc ? metalc5 B O GLU 98 B GLU 98 1_555 K NA NA . B NA 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? metalc ? metalc6 B O ILE 284 B ILE 284 1_555 K NA NA . B NA 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? # _chem_comp.formula 'C6 H14 O2' _chem_comp.formula_weight 118.174 _chem_comp.id MPD _chem_comp.mon_nstd_flag . _chem_comp.name (4S)-2-METHYL-2,4-PENTANEDIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C1 C2 MPD sing 286 n n C1 H11 MPD sing 287 n n C1 H12 MPD sing 288 n n C1 H13 MPD sing 289 n n C2 O2 MPD sing 290 n n C2 CM MPD sing 291 n n C2 C3 MPD sing 292 n n O2 HO2 MPD sing 293 n n CM HM1 MPD sing 294 n n CM HM2 MPD sing 295 n n CM HM3 MPD sing 296 n n C3 C4 MPD sing 297 n n C3 H31 MPD sing 298 n n C3 H32 MPD sing 299 n n C4 O4 MPD sing 300 n n C4 C5 MPD sing 301 n n C4 H4 MPD sing 302 n n O4 HO4 MPD sing 303 n n C5 H51 MPD sing 304 n n C5 H52 MPD sing 305 n n C5 H53 MPD sing 306 n n # _atom_sites.entry_id 2R86 _atom_sites.fract_transf_matrix[1][1] 0.008165 _atom_sites.fract_transf_matrix[1][2] 0.004714 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009428 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.001783 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 PO4 A 1 401 401 PO4 PO4 . D 2 PO4 A 1 402 402 PO4 PO4 . E 3 NA A 1 600 600 NA NA . F 4 ATP A 1 400 400 ATP ATP . G 5 MPD A 1 500 500 MPD MPD . H 5 MPD A 1 501 501 MPD MPD . I 2 PO4 B 1 401 401 PO4 PO4 . J 2 PO4 B 1 402 402 PO4 PO4 . K 3 NA B 1 600 600 NA NA . L 4 ATP B 1 400 400 ATP ATP . M 6 HOH A 1 601 1 HOH HOH . M 6 HOH A 2 602 2 HOH HOH . M 6 HOH A 3 603 3 HOH HOH . M 6 HOH A 4 604 4 HOH HOH . M 6 HOH A 5 605 5 HOH HOH . M 6 HOH A 6 606 6 HOH HOH . M 6 HOH A 7 607 7 HOH HOH . M 6 HOH A 8 608 8 HOH HOH . M 6 HOH A 9 609 10 HOH HOH . M 6 HOH A 10 610 11 HOH HOH . M 6 HOH A 11 611 13 HOH HOH . M 6 HOH A 12 612 14 HOH HOH . M 6 HOH A 13 613 15 HOH HOH . M 6 HOH A 14 614 16 HOH HOH . M 6 HOH A 15 615 17 HOH HOH . M 6 HOH A 16 616 20 HOH HOH . M 6 HOH A 17 617 21 HOH HOH . M 6 HOH A 18 618 22 HOH HOH . M 6 HOH A 19 619 23 HOH HOH . M 6 HOH A 20 620 24 HOH HOH . M 6 HOH A 21 621 25 HOH HOH . M 6 HOH A 22 622 26 HOH HOH . M 6 HOH A 23 623 28 HOH HOH . M 6 HOH A 24 624 29 HOH HOH . M 6 HOH A 25 625 30 HOH HOH . M 6 HOH A 26 626 31 HOH HOH . M 6 HOH A 27 627 33 HOH HOH . M 6 HOH A 28 628 34 HOH HOH . M 6 HOH A 29 629 37 HOH HOH . M 6 HOH A 30 630 38 HOH HOH . M 6 HOH A 31 631 40 HOH HOH . M 6 HOH A 32 632 41 HOH HOH . M 6 HOH A 33 633 44 HOH HOH . M 6 HOH A 34 634 45 HOH HOH . M 6 HOH A 35 635 46 HOH HOH . M 6 HOH A 36 636 47 HOH HOH . M 6 HOH A 37 637 52 HOH HOH . M 6 HOH A 38 638 53 HOH HOH . M 6 HOH A 39 639 54 HOH HOH . M 6 HOH A 40 640 57 HOH HOH . M 6 HOH A 41 641 58 HOH HOH . M 6 HOH A 42 642 59 HOH HOH . M 6 HOH A 43 643 60 HOH HOH . M 6 HOH A 44 644 61 HOH HOH . M 6 HOH A 45 645 62 HOH HOH . M 6 HOH A 46 646 63 HOH HOH . M 6 HOH A 47 647 66 HOH HOH . M 6 HOH A 48 648 69 HOH HOH . M 6 HOH A 49 649 70 HOH HOH . M 6 HOH A 50 650 71 HOH HOH . M 6 HOH A 51 651 72 HOH HOH . M 6 HOH A 52 652 73 HOH HOH . M 6 HOH A 53 653 74 HOH HOH . M 6 HOH A 54 654 75 HOH HOH . M 6 HOH A 55 655 76 HOH HOH . M 6 HOH A 56 656 77 HOH HOH . M 6 HOH A 57 657 79 HOH HOH . M 6 HOH A 58 658 85 HOH HOH . M 6 HOH A 59 659 86 HOH HOH . M 6 HOH A 60 660 88 HOH HOH . M 6 HOH A 61 661 93 HOH HOH . M 6 HOH A 62 662 94 HOH HOH . M 6 HOH A 63 663 95 HOH HOH . M 6 HOH A 64 664 96 HOH HOH . M 6 HOH A 65 665 97 HOH HOH . M 6 HOH A 66 666 98 HOH HOH . M 6 HOH A 67 667 99 HOH HOH . M 6 HOH A 68 668 100 HOH HOH . M 6 HOH A 69 669 101 HOH HOH . M 6 HOH A 70 670 106 HOH HOH . M 6 HOH A 71 671 108 HOH HOH . M 6 HOH A 72 672 109 HOH HOH . M 6 HOH A 73 673 110 HOH HOH . M 6 HOH A 74 674 111 HOH HOH . M 6 HOH A 75 675 112 HOH HOH . M 6 HOH A 76 676 113 HOH HOH . M 6 HOH A 77 677 114 HOH HOH . M 6 HOH A 78 678 116 HOH HOH . M 6 HOH A 79 679 117 HOH HOH . M 6 HOH A 80 680 118 HOH HOH . M 6 HOH A 81 681 119 HOH HOH . M 6 HOH A 82 682 121 HOH HOH . M 6 HOH A 83 683 122 HOH HOH . M 6 HOH A 84 684 124 HOH HOH . M 6 HOH A 85 685 125 HOH HOH . M 6 HOH A 86 686 126 HOH HOH . M 6 HOH A 87 687 127 HOH HOH . M 6 HOH A 88 688 128 HOH HOH . M 6 HOH A 89 689 129 HOH HOH . M 6 HOH A 90 690 130 HOH HOH . M 6 HOH A 91 691 132 HOH HOH . N 6 HOH B 1 601 9 HOH HOH . N 6 HOH B 2 602 12 HOH HOH . N 6 HOH B 3 603 18 HOH HOH . N 6 HOH B 4 604 19 HOH HOH . N 6 HOH B 5 605 27 HOH HOH . N 6 HOH B 6 606 32 HOH HOH . N 6 HOH B 7 607 35 HOH HOH . N 6 HOH B 8 608 36 HOH HOH . N 6 HOH B 9 609 39 HOH HOH . N 6 HOH B 10 610 42 HOH HOH . N 6 HOH B 11 611 43 HOH HOH . N 6 HOH B 12 612 48 HOH HOH . N 6 HOH B 13 613 49 HOH HOH . N 6 HOH B 14 614 50 HOH HOH . N 6 HOH B 15 615 51 HOH HOH . N 6 HOH B 16 616 55 HOH HOH . N 6 HOH B 17 617 56 HOH HOH . N 6 HOH B 18 618 64 HOH HOH . N 6 HOH B 19 619 65 HOH HOH . N 6 HOH B 20 620 67 HOH HOH . N 6 HOH B 21 621 68 HOH HOH . N 6 HOH B 22 622 78 HOH HOH . N 6 HOH B 23 623 80 HOH HOH . N 6 HOH B 24 624 81 HOH HOH . N 6 HOH B 25 625 82 HOH HOH . N 6 HOH B 26 626 83 HOH HOH . N 6 HOH B 27 627 84 HOH HOH . N 6 HOH B 28 628 87 HOH HOH . N 6 HOH B 29 629 89 HOH HOH . N 6 HOH B 30 630 90 HOH HOH . N 6 HOH B 31 631 91 HOH HOH . N 6 HOH B 32 632 92 HOH HOH . N 6 HOH B 33 633 102 HOH HOH . N 6 HOH B 34 634 103 HOH HOH . N 6 HOH B 35 635 104 HOH HOH . N 6 HOH B 36 636 105 HOH HOH . N 6 HOH B 37 637 107 HOH HOH . N 6 HOH B 38 638 115 HOH HOH . N 6 HOH B 39 639 120 HOH HOH . N 6 HOH B 40 640 123 HOH HOH . N 6 HOH B 41 641 131 HOH HOH . N 6 HOH B 42 642 133 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C1 MPD . . . H 5 54.457 48.656 -4.192 1 90.17 ? C1 MPD 501 A 1 HETATM 2 C C2 MPD . . . H 5 54.857 47.569 -3.201 1 90.06 ? C2 MPD 501 A 1 HETATM 3 O O2 MPD . . . H 5 53.823 47.487 -2.185 1 90.04 ? O2 MPD 501 A 1 HETATM 4 C CM MPD . . . H 5 56.167 47.956 -2.522 1 90.02 ? CM MPD 501 A 1 HETATM 5 C C3 MPD . . . H 5 55.024 46.233 -3.932 1 89.97 ? C3 MPD 501 A 1 HETATM 6 C C4 MPD . . . H 5 54.182 45.082 -3.382 1 89.81 ? C4 MPD 501 A 1 HETATM 7 O O4 MPD . . . H 5 54.62 44.75 -2.087 1 90.05 ? O4 MPD 501 A 1 HETATM 8 C C5 MPD . . . H 5 54.295 43.838 -4.253 1 89.52 ? C5 MPD 501 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 8 #